3NFB | pdb_00003nfb

Crystal structure of the N-terminal beta-aminopeptidase BapA in complex with hydrolyzed ampicillin

PDB DOI: https://doi.org/10.2210/pdb3NFB/pdb

Classification: Hydrolase/Inhibitor
Organism(s): Sphingosinicella xenopeptidilytica
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-06-10 Released: 2011-09-28
Deposition Author(s): Merz, T., Heck, T., Geueke, B., Kohler, H.-P.E., Gruetter, M.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.178 (Depositor), 0.180 (DCC)
R-Value Work:
0.150 (Depositor), 0.150 (DCC)
R-Value Observed:
0.151 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure and inhibition of the beta-aminopeptidase BapA, a new ampicillin-recognizing member of the N-terminal nucleophile hydrolase family

Heck, T., Merz, T., Geueke, B., Gruetter, M.G., Kohler, H.-P.E.

To be published.

Macromolecule Content

Total Structure Weight: 157.5 kDa
Atom Count: 12,103
Modeled Residue Count: 1,461
Deposited Residue Count: 1,492
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-peptidyl aminopeptidase	A, B, C, D	373	Sphingosinicella xenopeptidilytica	Mutation(s): 0 Gene Names: bapA EC: 3.4.11.25
UniProt
Find proteins for Q52VH2 (Sphingosinicella xenopeptidilytica) Explore Q52VH2 Go to UniProtKB: Q52VH2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q52VH2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OAE Query on OAE Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain J [auth B]	G [auth A] H [auth A] J [auth B] N [auth C] P [auth D] G [auth A], H [auth A], J [auth B], N [auth C], P [auth D], Q [auth D]	(2S,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid C₁₆ H₂₁ N₃ O₅ S KDAWOPKDXRJNHV-BLFANLJRSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain R [auth D] SDF format, chain O [auth C] SDF format, chain K [auth B] MOL2 format, chain I [auth A] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] MOL2 format, chain K [auth B] mmCIF format, chain I [auth A] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C] mmCIF format, chain K [auth B]	I [auth A], K [auth B], O [auth C], R [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain R [auth D] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain R [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain L [auth C] SDF format, chain M [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C]	E [auth A], F [auth A], L [auth C], M [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth C] Focus chain M [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth C] Focus chain M [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.178 (Depositor), 0.180 (DCC)
R-Value Work: 0.150 (Depositor), 0.150 (DCC)
R-Value Observed: 0.151 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.3	α = 90
b = 97.1	β = 108.7
c = 102.2	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-09-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-09-28
Type: Initial release
Version 1.1: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description